Chlamydia trachomatis (C. trachomatis) is the most common agent of sexually transmitted infections. The clinical spectrum of the disease ranges from urethritis to infertility in women and to trachoma. Intracellular localisation of the pathogen creates a challenge for routine diagnostics. In this review possible diagnostic tests have been presented, varying from classic cell culture analysis and serodiagnostics (Enzyme-linked Immunoassays, Indirect Immunofluorescence) to the most sophisticated nucleic acid analyses (hybridisation, Polymerase Chain Reaction, Transcription Mediated Amplification, Ligase Chain Reaction), Advantages and disadvantages of the leading tests are discussed. Possible reasons of false positive as well as false negative results of genetic testing are presented.